More than 98 per cent of voters have supported a new Egyptian constitution in a referendum, though voter turnout was lower than predicted, electoral officials say.

The overwhelming 'yes' vote advances a transition plan that the military-backed government unveiled after deposing Islamist president Mohammed Morsi last July following mass unrest over his rule.

"Now that God has supported us in legalising our constitution, we ask for his aid in achieving the remaining two stages of the road map: the presidential and parliamentary elections," said Nabil Salib, head of the Supreme Election Committee.

Officials say that 38.6 per cent of eligible voters took part in the ballot, well below the 55 per cent that an interior ministry official had earlier estimated.

However, it is still more than the 32.9 per cent turnout in a referendum in 2012 that backed the previous constitution under Mr Morsi's Muslim Brotherhood.

The Muslim Brotherhood, which has been designated a terrorist organisation by the government and faces a wide crackdown from security forces, boycotted the vote.

The new constitution could lead to an outright ban on Islamist parties and strengthens the political grip of the already powerful military establishment.

It also allows a presidential election to be held before parliamentary polls and interim president Adly Mansour, is expected to announce within days which election will come first.

Army chief General Abdel Fattah al-Sisi, who led the overthrow of Mr Morsi, is widely seen as the front-runner for the presidency.